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layout: default
navsection: userguide
title: "Using arv-copy"
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{% comment %}
Copyright (C) The Arvados Authors. All rights reserved.

SPDX-License-Identifier: CC-BY-SA-3.0
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{% include 'crunch1only_begin' %}
On those sites, the "copy a pipeline template" feature described below is not available. However, "copy a workflow" feature is not yet implemented.
{% include 'crunch1only_end' %}

This tutorial describes how to copy Arvados objects from one cluster to another by using @arv-copy@.

{% include 'tutorial_expectations' %}

h2. arv-copy

@arv-copy@ allows users to copy collections and pipeline templates from one cluster to another. By default, @arv-copy@ will recursively go through a template and copy all dependencies associated with the object.

For example, let's copy from the <a href="https://cloud.curoverse.com/">cloud instance *qr1hi*</a> to *dst_cluster*. The names *qr1hi* and *dst_cluster* are interchangable with any cluster name. You can find the cluster name from the prefix of the uuid of the object you want to copy. For example, in *qr1hi*-4zz18-tci4vn4fa95w0zx, the cluster name is qr1hi.

In order to communicate with both clusters, you must create custom configuration files for each cluster. In the Arvados Workbench, click on the dropdown menu icon <span class="fa fa-lg fa-user"></span> <span class="caret"></span> in the upper right corner of the top navigation menu to access the user settings menu, and click on the menu item *Current token*. Copy the @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ in both of your clusters. Then, create two configuration files, one for each cluster. The names of the files must have the format of *uuid_prefix.conf*. In our example, let's make two files, one for *qr1hi* and one for *dst_cluster*. From your *Current token* page in *qr1hi* and *dst_cluster*, copy the @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@.

!{display: block;margin-left: 25px;margin-right: auto;}{{ site.baseurl }}/images/api-token-host.png!

Copy your @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ into the config files as shown below in the shell account from which you are executing the commands. For example, the default shell you may have access to is shell.qr1hi. You can add these files in ~/.config/arvados/ in the qr1hi shell terminal.

<notextile>
<pre><code>~$ <span class="userinput">cd ~/.config/arvados</span>
~$ <span class="userinput">echo "ARVADOS_API_HOST=qr1hi.arvadosapi.com" >> qr1hi.conf</span>
~$ <span class="userinput">echo "ARVADOS_API_TOKEN=123456789abcdefghijkl" >> qr1hi.conf</span>
~$ <span class="userinput">echo "ARVADOS_API_HOST=dst_cluster.arvadosapi.com" >> dst_cluster.conf</span>
~$ <span class="userinput">echo "ARVADOS_API_TOKEN=987654321lkjihgfedcba" >> dst_cluster.conf</span>
</code></pre>
</notextile>

Now you're ready to copy between *qr1hi* and *dst_cluster*!

h3. How to copy a collection

First, select the uuid of the collection you want to copy from the source cluster. The uuid can be found in the collection display page in the collection summary area (top left box), or from the URL bar (the part after @collections/...@)

Now copy the collection from *qr1hi* to *dst_cluster*. We will use the uuid @qr1hi-4zz18-tci4vn4fa95w0zx@ as an example. You can find this collection in the <a href="https://cloud.curoverse.com/collections/qr1hi-4zz18-tci4vn4fa95w0zx">lobSTR v.3 project on cloud.curoverse.com</a>.
<notextile>
<pre><code>~$ <span class="userinput">arv-copy --src qr1hi --dst dst_cluster qr1hi-4zz18-tci4vn4fa95w0zx</span>
qr1hi-4zz18-tci4vn4fa95w0zx: 6.1M / 6.1M 100.0%
arvados.arv-copy[1234] INFO: Success: created copy with uuid dst_cluster-4zz18-8765943210cdbae
</code></pre>
</notextile>

The output of arv-copy displays the uuid of the collection generated in the destination cluster. By default, the output is placed in your home project in the destination cluster. If you want to place your collection in a pre-created project, you can specify the project you want it to be in using the tag @--project-uuid@ followed by the project uuid.

For example, this will copy the collection to project dst_cluster-j7d0g-a894213ukjhal12 in the destination cluster.

<notextile> <pre><code>~$ <span class="userinput">arv-copy --src qr1hi --dst dst_cluster --project-uuid dst_cluster-j7d0g-a894213ukjhal12 qr1hi-4zz18-tci4vn4fa95w0zx</span>
</code></pre>
</notextile>

h3. How to copy a pipeline template

{% include 'arv_copy_expectations' %}

We will use the uuid @qr1hi-p5p6p-9pkaxt6qjnkxhhu@ as an example pipeline template.

<notextile>
<pre><code>~$ <span class="userinput">arv-copy --src qr1hi --dst dst_cluster --dst-git-repo $USER/tutorial qr1hi-p5p6p-9pkaxt6qjnkxhhu</span>
To git@git.dst_cluster.arvadosapi.com:$USER/tutorial.git
 * [new branch] git_git_qr1hi_arvadosapi_com_arvados_git_ac21f0d45a76294aaca0c0c0fdf06eb72d03368d -> git_git_qr1hi_arvadosapi_com_arvados_git_ac21f0d45a76294aaca0c0c0fdf06eb72d03368d
arvados.arv-copy[19694] INFO: Success: created copy with uuid dst_cluster-p5p6p-rym2h5ub9m8ofwj
</code></pre>
</notextile>

New branches in the destination git repo will be created for each branch used in the pipeline template. For example, if your source branch was named ac21f0d45a76294aaca0c0c0fdf06eb72d03368d, your new branch will be named @git_git_qr1hi_arvadosapi_com_reponame_git_ac21f0d45a76294aaca0c0c0fdf06eb72d03368d@.

By default, if you copy a pipeline template recursively, you will find that the template as well as all the dependencies are in your home project.

If you would like to copy the object without dependencies, you can use the @--no-recursive@ tag.

For example, we can copy the same object using this tag.

<notextile>
<pre><code>~$ <span class="userinput">arv-copy --src qr1hi --dst dst_cluster --dst-git-repo $USER/tutorial --no-recursive qr1hi-p5p6p-9pkaxt6qjnkxhhu</span>
</code></pre>
</notextile>

h3. How to copy a workflow

We will use the uuid @zzzzz-7fd4e-sampleworkflow1@ as an example workflow.

<notextile>
<pre><code>~$ <span class="userinput">arv-copy --src zzzzz --dst dst_cluster --dst-git-repo $USER/tutorial zzzzz-7fd4e-sampleworkflow1</span>
zzzzz-4zz18-jidprdejysravcr: 1143M / 1143M 100.0%
2017-01-04 04:11:58 arvados.arv-copy[5906] INFO:
2017-01-04 04:11:58 arvados.arv-copy[5906] INFO: Success: created copy with uuid dst_cluster-7fd4e-ojtgpne594ubkt7
</code></pre>
</notextile>

The name, description, and workflow definition from the original workflow will be used for the destination copy. In addition, any *locations* and *docker images* found in the src workflow definition will also be copied to the destination recursively.

If you would like to copy the object without dependencies, you can use the @--no-recursive@ flag.

For example, we can copy the same object non-recursively using the following:

<notextile>
<pre><code>~$ <span class="userinput">arv-copy --src zzzzz --dst dst_cluster --dst-git-repo $USER/tutorial --no-recursive zzzzz-7fd4e-sampleworkflow1</span>
</code></pre>
</notextile>